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- PDB-3ws1: N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER S... -

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Basic information

Entry
Database: PDB / ID: 3ws1
TitleN288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-1B)
ComponentsBeta-lactamase
KeywordsHYDROLASE / CEPHALOSPORINASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChromohalobacter sp. 560 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Tokunaga, H. / Ishibashi, M. ...Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Tokunaga, M. / Kuroki, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of a highly acidic beta-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site
Authors: Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shibazaki, C. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Kawamoto, M. / Tokunaga, H. / Ishibashi, M. / Blaber, M. / Tokunaga, M. / Kuroki, R.
History
DepositionFeb 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,45515
Polymers118,7883
Non-polymers66712
Water10,467581
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8896
Polymers39,5961
Non-polymers2935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7164
Polymers39,5961
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8495
Polymers39,5961
Non-polymers2534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.125, 115.125, 67.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASPAA8 - 3658 - 365
21GLNGLNASPASPBB8 - 3658 - 365
12GLNGLNASPASPAA8 - 3658 - 365
22GLNGLNASPASPCC8 - 3658 - 365
13ARGARGVALVALBB7 - 3667 - 366
23ARGARGVALVALCC7 - 3667 - 366

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Beta-lactamase


Mass: 39596.098 Da / Num. of mol.: 3 / Fragment: UNP residues 22-388 / Mutation: N288Q, N321Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter sp. 560 (bacteria) / Gene: bla / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI BL21 STAR (DE3) / References: UniProt: Q76LX5, beta-lactamase
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG8000. Obtained crystal was soaked into a solution containing 100mM MES NaOH ...Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG8000. Obtained crystal was soaked into a solution containing 100mM MES NaOH buffer (pH 6.5), 200mM Ca acetate hydrate, 75mM NaCl, 25mM CsCl and 18% PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SAGA-LS / Beamline: BL07 / Wavelength: 1.000, 2.166
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.1661
ReflectionResolution: 1.8→50 Å / Num. obs: 92243 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.78 / % possible all: 98.4

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Processing

Software
NameClassification
CrystalCleardata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WRZ

3wrz


Resolution: 1.8→37.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.356 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21118 4618 5 %RANDOM
Rwork0.18519 ---
obs0.18648 87677 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8186 0 12 581 8779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198380
X-RAY DIFFRACTIONr_bond_other_d0.0060.027865
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9811432
X-RAY DIFFRACTIONr_angle_other_deg1.218318145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4151083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.124.69371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.343151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9071555
X-RAY DIFFRACTIONr_chiral_restr0.0860.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219631
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021758
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9371.2934323
X-RAY DIFFRACTIONr_mcbond_other0.9371.2924322
X-RAY DIFFRACTIONr_mcangle_it1.5351.9315400
X-RAY DIFFRACTIONr_mcangle_other1.5351.9325401
X-RAY DIFFRACTIONr_scbond_it1.2971.4724057
X-RAY DIFFRACTIONr_scbond_other1.2971.4734058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0432.1526030
X-RAY DIFFRACTIONr_long_range_B_refined5.2911.4199984
X-RAY DIFFRACTIONr_long_range_B_other5.24710.9729717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A216040.09
12B216040.09
21A220100.08
22C220100.08
31B216400.1
32C216400.1
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 341 -
Rwork0.204 6411 -
obs--98.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3042-0.0960.16391.2216-0.43332.1357-0.00460.0520.0065-0.1153-0.0407-0.16420.14370.08790.04530.04580.02850.01860.02170.00570.0252-42.405820.68810.7177
21.7274-0.91240.38283.4324-0.20991.62530.02970.10270.31750.2753-0.3317-0.7559-0.01020.08290.3020.0318-0.0404-0.05830.16770.17970.3319-47.8043-15.799927.0913
31.3905-0.68330.41491.58710.27482.13950.16180.10650.1498-0.1972-0.0959-0.0694-0.0168-0.0223-0.0660.0360.01770.02660.01050.01480.0348-7.740818.5149-28.0307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 367
2X-RAY DIFFRACTION2B7 - 366
3X-RAY DIFFRACTION3C7 - 366

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